They didn't build in any way of reprogramming a spaceship AI from outside the spaceship because if they had, it would be used by their enemies.
They didn't build in any requirements to shut down into a spaceship's AI because if they had, it might not fight their enemies after a crew-wipe.
They didn't build in any way for a spaceships AI to get creative in its targeting programs because if they had, it might decide an enemy wasn't an enemy.
They didn't build a spaceship AI that understood changes in ship design because they didn't foresee themselves being targeted.
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